James Procter <j.procter@dundee.ac.uk>: Author Summary
| Build | Completed | Code commits | Tests |
|---|---|---|---|
| JB › GDBI › #21 | 6 months ago |
Merge branch 'bug/JAL-4186_space_in_sequence_name_causes_empty_modal' into develop
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Testless build |
| JB › GDC › #185 | 2 days ago |
JAL-4356 bump RELEASE
Merge branch 'patch/JAL-840_clustalx_docs_fix' into develop
JAL-840 generate fragments of clustal.html documentation via ClustalxColurSchemeTest.testDocString()
JAL-840 updated docs - thanks to AMW for verifying by independent implementation over at https://swissmodel.expasy.org/docs/help#clustalColours
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Testless build |
| JB › GPC › #276 | 2 days ago |
JAL-4356 bump RELEASE
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Testless build |
| JB › GDB › #606 | 2 days ago |
JAL-4356 bump RELEASE
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1683 passed |
| JB › GPC › #275 | 2 days ago |
Merge branch 'patch/JAL-840_clustalx_docs_fix' into develop
JAL-840 generate fragments of clustal.html documentation via ClustalxColurSchemeTest.testDocString()
JAL-840 updated docs - thanks to AMW for verifying by independent implementation over at https://swissmodel.expasy.org/docs/help#clustalColours
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Testless build |
| JB › GJB › #387 | 2 days ago |
JAL-4356 bump RELEASE
|
Testless build |
| JB › GDB › #605 | 2 days ago |
JAL-840 updated docs - thanks to AMW for verifying by independent implementation over at https://swissmodel.expasy.org/docs/help#clustalColours
JAL-840 generate fragments of clustal.html documentation via ClustalxColurSchemeTest.testDocString()
Merge branch 'patch/JAL-840_clustalx_docs_fix' into develop
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1683 passed |
| JB › GJB › #386 | 2 days ago |
Merge branch 'patch/JAL-840_clustalx_docs_fix' into develop
JAL-840 updated docs - thanks to AMW for verifying by independent implementation over at https://swissmodel.expasy.org/docs/help#clustalColours
JAL-840 generate fragments of clustal.html documentation via ClustalxColurSchemeTest.testDocString()
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Testless build |
| JB › GDC › #184 | 1 week ago |
JAL-4343 fix insufficient-caffeine error - add whats new for 2.11.3.1
Merge branch 'bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square-FIXED_from_develop' into develop
Merge branch 'patch/JAL-4342_emptyannotationsexport' into develop
Merge branch 'patch/JAL-4345_pae_epas1_doubleclick' into develop
JAL-4345 patch and release notes
JAL-4351 2.11.3.2 scheduled for 1st December release
JAL-4342 test and patch checking annotation csv export contains the annotations on the alignment or a specific exported annotation
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Testless build |
| JB › GGR › #7 | 8 months ago |
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - and fix up a casting issue (again?)
Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4133 store/restore alignment view’s charWidth and charHeight in Jalview project
Merge branch 'features/JAL-3858_PAEsInProjects' into develop
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
JAL-3858 construct a PAE direct from float array
JAL-3858 JAL-2381 allow different linear shading schemes for selected/non-selected regions of contact matrix heat map
JAL-4090 Release 2.11.3.0 release notes and version bump
JAL-1713 update from Jalview 2.11.3 develop Merge branch 'develop' into feature/JAL-1713_overviewInProject regenerated jaxb classes to resolve conflicts
JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX annotation.graph type, with actual matrix type stored in calcId
JAL-629 don’t complain for Unary args
JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version
JAL-4095 slightly better threshold setting and todos for improvement
JAL-629 suggest not breaking out of the structure processing loop if just one structure has a bunk sequence association..
JAL-4133 update validChar width when font is changed so characters are suppressed for small widths
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
JAL-1551 source formatting
JAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequence annotation
JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
JAL-629 labelled breaks are frowned upon by everyone
JAL-3858 new MatrixType JAX-RI POJO
JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset sequence annotation. Rudimentary tests.
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts: src/jalview/bin/Jalview.java JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
JAL-629 don’t trash user’s system property file when adjusting settings to process CL args
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure itself at construction time
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts: src/jalview/bin/Jalview.java Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - additional test case
JAL-3858 simple test for PAE matrix recovery
JAL-1551 remove temp file in src
JAL-629 make sure we show GUI when not driven programmatically
JAL-4095 magic fill behaviour is PAE specific
JAL-629 don’t carry on Jalview.main if we’ve already processed command line args another way
|
Testless build |
| Build | Completed | Code commits | Tests |
|---|---|---|---|
| JB › GGR › #7 | 8 months ago |
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - and fix up a casting issue (again?)
Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4133 store/restore alignment view’s charWidth and charHeight in Jalview project
Merge branch 'features/JAL-3858_PAEsInProjects' into develop
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
JAL-3858 construct a PAE direct from float array
JAL-3858 JAL-2381 allow different linear shading schemes for selected/non-selected regions of contact matrix heat map
JAL-4090 Release 2.11.3.0 release notes and version bump
JAL-1713 update from Jalview 2.11.3 develop Merge branch 'develop' into feature/JAL-1713_overviewInProject regenerated jaxb classes to resolve conflicts
JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX annotation.graph type, with actual matrix type stored in calcId
JAL-629 don’t complain for Unary args
JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version
JAL-4095 slightly better threshold setting and todos for improvement
JAL-629 suggest not breaking out of the structure processing loop if just one structure has a bunk sequence association..
JAL-4133 update validChar width when font is changed so characters are suppressed for small widths
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
JAL-1551 source formatting
JAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequence annotation
JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
JAL-629 labelled breaks are frowned upon by everyone
JAL-3858 new MatrixType JAX-RI POJO
JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset sequence annotation. Rudimentary tests.
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts: src/jalview/bin/Jalview.java JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
JAL-629 don’t trash user’s system property file when adjusting settings to process CL args
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure itself at construction time
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts: src/jalview/bin/Jalview.java Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - additional test case
JAL-3858 simple test for PAE matrix recovery
JAL-1551 remove temp file in src
JAL-629 make sure we show GUI when not driven programmatically
JAL-4095 magic fill behaviour is PAE specific
JAL-629 don’t carry on Jalview.main if we’ve already processed command line args another way
|
Testless build |
| Build | Completed | Code commits | Tests |
|---|